Evolving Cellular Automata Schemes for Protein Folding Modeling Using the Rosetta Atomic Representation

Financiado para publicación en acceso aberto: Universidade da Coruña/CISUG [Abstract] Protein folding is the dynamic process by which a protein folds into its final native structure. This is different to the traditional problem of the prediction of the final protein structure, since it requires a modeling of how protein components interact over time to obtain the final folded structure. In this study we test whether a model of the folding process can be obtained exclusively through machine learning. To this end, protein folding is considered as an emergent process and the cellular automata tool is used to model the folding process. A neural cellular automaton is defined, using a connectionist model that acts as a cellular automaton through the protein chain to define the dynamic folding. Differential evolution is used to automatically obtain the optimized neural cellular automata that provide protein folding. We tested the methods with the Rosetta coarse-grained atomic model of protein representation, using different proteins to analyze the modeling of folding and the structure refinement that the modeling can provide, showing the potential advantages that such methods offer, but also difficulties that arise.This study was funded by the Xunta de Galicia and the European Union (European Regional Development Fund - Galicia 2014-2020 Program), with grants CITIC (ED431G 2019/01), GPC ED431B 2019/03 and IN845D-02 (funded by the “Agencia Gallega de Innovación”, co-financed by Feder funds), and by the Spanish Ministry of Science and Innovation (project PID2020-116201GB-I00). Open Access funding provided thanks to the CRUE-CSIC agreement with Springer NatureXunta de Galicia; ED431G 2019/01Xunta de Galicia; ED431B 2019/03Xunta de Galicia; IN845D-0

A complex systems approach to education in Switzerland

The insights gained from the study of complex systems in biological, social, and engineered systems enables us not only to observe and understand, but also to actively design systems which will be capable of successfully coping with complex and dynamically changing situations. The methods and mindset required for this approach have been applied to educational systems with their diverse levels of scale and complexity. Based on the general case made by Yaneer Bar-Yam, this paper applies the complex systems approach to the educational system in Switzerland. It confirms that the complex systems approach is valid. Indeed, many recommendations made for the general case have already been implemented in the Swiss education system. To address existing problems and difficulties, further steps are recommended. This paper contributes to the further establishment complex systems approach by shedding light on an area which concerns us all, which is a frequent topic of discussion and dispute among politicians and the public, where billions of dollars have been spent without achieving the desired results, and where it is difficult to directly derive consequences from actions taken. The analysis of the education system's different levels, their complexity and scale will clarify how such a dynamic system should be approached, and how it can be guided towards the desired performance

Using MapReduce Streaming for Distributed Life Simulation on the Cloud

Distributed software simulations are indispensable in the study of large-scale life models but often require the use of technically complex lower-level distributed computing frameworks, such as MPI. We propose to overcome the complexity challenge by applying the emerging MapReduce (MR) model to distributed life simulations and by running such simulations on the cloud. Technically, we design optimized MR streaming algorithms for discrete and continuous versions of Conway’s life according to a general MR streaming pattern. We chose life because it is simple enough as a testbed for MR’s applicability to a-life simulations and general enough to make our results applicable to various lattice-based a-life models. We implement and empirically evaluate our algorithms’ performance on Amazon’s Elastic MR cloud. Our experiments demonstrate that a single MR optimization technique called strip partitioning can reduce the execution time of continuous life simulations by 64%. To the best of our knowledge, we are the first to propose and evaluate MR streaming algorithms for lattice-based simulations. Our algorithms can serve as prototypes in the development of novel MR simulation algorithms for large-scale lattice-based a-life models.https://digitalcommons.chapman.edu/scs_books/1014/thumbnail.jp

Autopoietic-extended architecture: can buildings think?

To incorporate bioremedial functions into the performance of buildings and to balance generative architecture's dominant focus on computational programming and digital fabrication, this thesis first hybridizes theories of autopoiesis into extended cognition in order to research biological domains that include synthetic biology and biocomputation. Under the rubric of living technology I survey multidisciplinary fields to gather perspective for student design of bioremedial and/or metabolic components in generative architecture where generative not only denotes the use of computation but also includes biochemical, biomechanical, and metabolic functions. I trace computation and digital simulations back to Alan Turing's early 1950s Morphogenetic drawings, reaction-diffusion algorithms, and pioneering artificial intelligence (AI) in order to establish generative architecture's point of origin. I ask provocatively: Can buildings think? as a question echoing Turing's own "Can machines think?" Thereafter, I anticipate not only future bioperformative materials but also theories capable of underpinning strains of metabolic intelligences made possible via AI, synthetic biology, and living technology. I do not imply that metabolic architectural intelligence will be like human cognition. I suggest, rather, that new research and pedagogies involving the intelligence of bacteria, plants, synthetic biology, and algorithms define approaches that generative architecture should take in order to source new forms of autonomous life that will be deployable as corrective environmental interfaces. I call the research protocol autopoietic-extended design, theorizing it as an operating system (OS), a research methodology, and an app schematic for design studios and distance learning that makes use of in-field, e-, and m-learning technologies. A quest of this complexity requires scaffolding for coordinating theory-driven teaching with practice-oriented learning. Accordingly, I fuse Maturana and Varela's biological autopoiesis and its definitions of minimal biological life with Andy Clark's hypothesis of extended cognition and its cognition-to-environment linkages. I articulate a generative design strategy and student research method explained via architectural history interpreted from Louis Sullivan's 1924 pedagogical drawing system, Le Corbusier's Modernist pronouncements, and Greg Lynn's Animate Form. Thus, autopoietic-extended design organizes thinking about the generation of ideas for design prior to computational production and fabrication, necessitating a fresh relationship between nature/science/technology and design cognition. To systematize such a program requires the avoidance of simple binaries (mind/body, mind/nature) as well as the stationing of tool making, technology, and architecture within the ream of nature. Hence, I argue, in relation to extended phenotypes, plant-neurobiology, and recent genetic research: Consequently, autopoietic-extended design advances design protocols grounded in morphology, anatomy, cognition, biology, and technology in order to appropriate metabolic and intelligent properties for sensory/response duty in buildings. At m-learning levels smartphones, social media, and design apps source data from nature for students to mediate on-site research by extending 3D pedagogical reach into new university design programs. I intend the creation of a dialectical investigation of animal/human architecture and computational history augmented by theory relevant to current algorithmic design and fablab production. The autopoietic-extended design dialectic sets out ways to articulate opposition/differences outside the Cartesian either/or philosophy in order to prototype metabolic architecture, while dialectically maintaining: Buildings can think

Evolutionary Computation

This book presents several recent advances on Evolutionary Computation, specially evolution-based optimization methods and hybrid algorithms for several applications, from optimization and learning to pattern recognition and bioinformatics. This book also presents new algorithms based on several analogies and metafores, where one of them is based on philosophy, specifically on the philosophy of praxis and dialectics. In this book it is also presented interesting applications on bioinformatics, specially the use of particle swarms to discover gene expression patterns in DNA microarrays. Therefore, this book features representative work on the field of evolutionary computation and applied sciences. The intended audience is graduate, undergraduate, researchers, and anyone who wishes to become familiar with the latest research work on this field

Proceedings, MSVSCC 2014

Proceedings of the 8th Annual Modeling, Simulation & Visualization Student Capstone Conference held on April 17, 2014 at VMASC in Suffolk, Virginia

Deep Model for Improved Operator Function State Assessment

A deep learning framework is presented for engagement assessment using EEG signals. Deep learning is a recently developed machine learning technique and has been applied to many applications. In this paper, we proposed a deep learning strategy for operator function state (OFS) assessment. Fifteen pilots participated in a flight simulation from Seattle to Chicago. During the four-hour simulation, EEG signals were recorded for each pilot. We labeled 20- minute data as engaged and disengaged to fine-tune the deep network and utilized the remaining vast amount of unlabeled data to initialize the network. The trained deep network was then used to assess if a pilot was engaged during the four-hour simulation

Automated evolutionary design of self-assembly and self-organising systems

Self-assembly and self-organisation are natural construction processes where the spontaneous formation of aggregates emerges throughout the progressive interplay of local interactions among its constituents. Made upon cooperative self-reliant components, self-assembly and self-organising systems are seen as distributed, not necessarily synchronous, autopoietic mechanisms for the bottom-up fabrication of supra-structures. The systematic understanding of how nature endows these autonomous components with sufficient ''intelligence'' to combine themselves to form useful aggregates brings challenging questions to science, answers to which have many potential applications in matters of life and technological advances. It is for this reason that the investigation to be presented along this thesis focuses on the automated design of self-assembly and self-organising systems by means of artificial evolution. Towards this goal, this dissertation embodies research on evolutionary algorithms applied to the parameters design of a computational model of self-organisation and the components design of a computational model of self-assembly. In addition, an analytical assessment combining correlation metrics and clustering, as well as the exploration of emergent patterns of cooperativity and the measurement of activity across evolution, is made. The results support the research hypothesis that an adaptive process such as artificial evolution is indeed a suitable strategy for the automated design of self-assembly and self-organising systems where local interactions, homogeneity and both stochastic and discrete models of execution play a crucial role in emergent complex structures